diff --git a/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/trinity/_index.md b/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/trinity/_index.md
index 6e19c01b92c0ca5ce254080247c7e0e73c9154b3..4d912274f1fbb39df0b176ad9dd7a45999525ad6 100644
--- a/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/trinity/_index.md
+++ b/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/trinity/_index.md
@@ -14,6 +14,10 @@ $ Trinity --seqType [fa|fq] --max_memory <maximum_memory> --left input_reads_pai
 {{< /highlight >}}
 where **input_reads_pair_1.[fa|fq]** and **input_reads_pair_2.[fa|fq]** are the input paired-end files of sequence reads in fasta/fastq format, and **--seqType** is the type of these input reads. The option **--max_memory** specifies the maximum memory to use with Trinity.
 
+{{% notice info %}}
+**Trinity produces many intermediate files that can affect the file system. To avoid any issues, please copy all the input data to the faster local storage called "scratch", store the output in "scratch" and finally copy all the needed output files from "scratch" to /work. The "scratch" directories are unique per job and are deleted when the job finishes. This can greatly improve performance!**
+{{% /notice %}}
+
 Additional Trinity **options** can be found in the Trinity website, or by typing:
 {{< highlight bash >}}
 $ Trinity
diff --git a/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/trinity/running_trinity_in_multiple_steps.md b/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/trinity/running_trinity_in_multiple_steps.md
index 22fa8383adcd446328cf2e6a354bc5035e77ac13..75137592a6dfb86993ed1f8c12c4317f3a5b5b36 100644
--- a/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/trinity/running_trinity_in_multiple_steps.md
+++ b/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/trinity/running_trinity_in_multiple_steps.md
@@ -7,6 +7,10 @@ weight = "10"
 
 ## Running Trinity with Paired-End fastq data with 8 CPUs and 100GB of RAM
 
+{{% notice info %}}
+**Trinity produces many intermediate files that can affect the file system. To avoid any issues, please copy all the input data to the faster local storage called "scratch", store the output in "scratch" and finally copy all the needed output files from "scratch" to /work. The "scratch" directories are unique per job and are deleted when the job finishes. This can greatly improve performance!**
+{{% /notice %}}
+
 The first step of running Trinity is to run Trinity with the option **--no_run_inchworm**:
 {{% panel header="`trinity_step1.submit`"%}}
 {{< highlight bash >}}
@@ -21,7 +25,14 @@ The first step of running Trinity is to run Trinity with the option **--no_run_i
 
 module load trinity
 
-Trinity --seqType fq --max_memory 100G --left input_reads_pair_1.fastq --right input_reads_pair_2.fastq --SS_lib_type FR --output trinity_out/ --CPU $SLURM_NTASKS_PER_NODE --no_run_inchworm
+# copy input data to /scratch
+cp input_reads_pair_1.fastq /scratch
+cp input_reads_pair_2.fastq /scratch 
+
+Trinity --seqType fq --max_memory 100G --left /scratch/input_reads_pair_1.fastq --right /scratch/input_reads_pair_2.fastq --SS_lib_type FR --output /scratch/trinity_out/ --CPU $SLURM_NTASKS_PER_NODE --no_run_inchworm
+
+# copy output in current directory
+cp -r /scratch/trinity_out/ .
 {{< /highlight >}}
 {{% /panel %}}
 
@@ -40,7 +51,15 @@ The second step of running Trinity is to run Trinity with the option **--no_run_
 
 module load trinity
 
-Trinity --seqType fq --max_memory 100G --left input_reads_pair_1.fastq --right input_reads_pair_2.fastq --SS_lib_type FR --output trinity_out/ --CPU $SLURM_NTASKS_PER_NODE --no_run_chrysalis
+# copy input data to /scratch
+cp input_reads_pair_1.fastq /scratch
+cp input_reads_pair_2.fastq /scratch
+cp -r trinity_out /scratch/
+
+Trinity --seqType fq --max_memory 100G --left /scratch/input_reads_pair_1.fastq --right /scratch/input_reads_pair_2.fastq --SS_lib_type FR --output /scratch/trinity_out/ --CPU $SLURM_NTASKS_PER_NODE --no_run_chrysalis
+
+# copy output in current directory
+cp -r /scratch/trinity_out/ .
 {{< /highlight >}}
 {{% /panel %}}
 
@@ -59,7 +78,15 @@ The third step of running Trinity is to run Trinity with the option **--no_distr
 
 module load trinity
 
-Trinity --seqType fq --max_memory 100G --left input_reads_pair_1.fastq --right input_reads_pair_2.fastq --SS_lib_type FR --output trinity_out/ --CPU $SLURM_NTASKS_PER_NODE --no_distributed_trinity_exec
+# copy input data to /scratch
+cp input_reads_pair_1.fastq /scratch
+cp input_reads_pair_2.fastq /scratch
+cp -r trinity_out /scratch/
+
+Trinity --seqType fq --max_memory 100G --left /scratch/input_reads_pair_1.fastq --right /scratch/input_reads_pair_2.fastq --SS_lib_type FR --output /scratch/trinity_out/ --CPU $SLURM_NTASKS_PER_NODE --no_distributed_trinity_exec
+
+# copy output in current directory
+cp -r /scratch/trinity_out/ .
 {{< /highlight >}}
 {{% /panel %}}
 
@@ -78,7 +105,15 @@ The fourth step of running Trinity is to run Trinity without any additional opti
 
 module load trinity
 
-Trinity --seqType fq --max_memory 100G --left input_reads_pair_1.fastq --right input_reads_pair_2.fastq --SS_lib_type FR --output trinity_out/ --CPU $SLURM_NTASKS_PER_NODE
+# copy input data to /scratch
+cp input_reads_pair_1.fastq /scratch
+cp input_reads_pair_2.fastq /scratch
+cp -r trinity_out /scratch/
+
+Trinity --seqType fq --max_memory 100G --left /scratch/input_reads_pair_1.fastq --right /scratch/input_reads_pair_2.fastq --SS_lib_type FR --output /scratch/trinity_out/ --CPU $SLURM_NTASKS_PER_NODE
+
+# copy output in current directory
+cp -r /scratch/trinity_out/ .
 {{< /highlight >}}
 {{% /panel %}}